We’re soliciting feedback from JGI primary and data users on JGI Data Release and Utilization policies. Fill out our Request for Information by April 21.
Info • Russula earlei BPL698 v1.0

Status

[June 2019] The Russula earlei genome was extracted from a metagenomic sample consisting of the fungus and several bacterial species. The sample was sequenced with PacBio and assembled with Falcon. The fungal genome was then annotated with the JGI Annotation Pipeline. The mitochondrial genome was assembled separately and is available on the Download page. The co-isolated bacterial genomes of Collimonas pratensis and Bradyrhizobium sp. 1108993 were also assembled separately and are also available on the Download page.

The metatranscriptomic sample was sequenced with Illumina and assembled with Trinity. Unlike the metagenome, the metatranscriptome was not separated into its constituent species compartments, and thus mapped relatively poorly to the fungal genome.

Summary statistics for the Russula earlei BPL698 v1.0 release are below.
Genome Assembly
Genome Assembly size (Mbp) 70.01
Sequencing read coverage depth 82.88x
# of contigs 2010
# of scaffolds 2010
# of scaffolds >= 2Kbp 1938
Scaffold N50 238
Scaffold L50 (Mbp) 0.08
# of gaps 0
% of scaffold length in gaps 0.0%
Three largest Scaffolds (Mbp) 0.61, 0.51, 0.49


ESTs Data set # sequences total # mapped to genome % mapped to genome
Ests est.fasta 118186317 113581031 96.1%
Other JGI_RNA_contigs 159231 73491 46.2%


Gene Models FilteredModels1
length (bp) of: average median
gene 1655 1385
transcript 1363 1127
exon 260 160
intron 71 58
description:
protein length (aa) 397 313
exons per gene 5.24 4
# of gene models 12153


Funding

The work conducted by the U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231.